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Use WritablePropertyMap #971

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merged 1 commit into from
Oct 2, 2024
Merged

Use WritablePropertyMap #971

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31 changes: 17 additions & 14 deletions src/org/labkey/targetedms/TargetedMSController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -77,6 +77,8 @@
import org.labkey.api.data.DataRegion;
import org.labkey.api.data.DbScope;
import org.labkey.api.data.PropertyManager;
import org.labkey.api.data.PropertyManager.PropertyMap;
import org.labkey.api.data.PropertyManager.WritablePropertyMap;
import org.labkey.api.data.RenderContext;
import org.labkey.api.data.SQLFragment;
import org.labkey.api.data.SimpleFilter;
Expand Down Expand Up @@ -751,12 +753,12 @@ public Object execute(LeveyJenningsPlotOptions form, BindException errors)
{
ApiSimpleResponse response = new ApiSimpleResponse();

PropertyManager.PropertyMap properties = null;
PropertyMap properties = null;

// only stash and retrieve plot option properties for logged in users
// only stash and retrieve plot option properties for logged-in users
if (!getUser().isGuest())
{
properties = PropertyManager.getWritableProperties(getUser(), getContainer(), QCFolderConstants.CATEGORY, true);
WritablePropertyMap writable = PropertyManager.getWritableProperties(getUser(), getContainer(), QCFolderConstants.CATEGORY, true);

Map<String, String> valuesToPersist = form.getAsMapOfStrings();
if (!valuesToPersist.isEmpty())
Expand All @@ -766,20 +768,21 @@ public Object execute(LeveyJenningsPlotOptions form, BindException errors)
valuesToPersist.put("endDate", form.getEndDate());
valuesToPersist.put("selectedAnnotations", form.getSelectedAnnotationsString());

properties.putAll(valuesToPersist);
properties.save();
writable.putAll(valuesToPersist);
writable.save();
}
else
{
if (properties.containsKey("selectedAnnotations") && (ReplicateManager.getReplicateAnnotationNameValues(getContainer()).size() == 0))
if (writable.containsKey("selectedAnnotations") && (ReplicateManager.getReplicateAnnotationNameValues(getContainer()).isEmpty()))
{
// If there are no replicate annotations in this folder anymore, remove any saved annotation filters
// Issue 35726: No way to clear previously saved replicate annotation values in QC plots if folder no longer contains annotations
properties.remove("selectedAnnotations");
properties.save();
writable.remove("selectedAnnotations");
writable.save();
}
}

properties = writable;
}

if (properties == null || properties.isEmpty())
Expand All @@ -802,8 +805,8 @@ public static class SaveQCPlotSettingsAsDefaultAction extends MutatingApiAction<
@Override
public Object execute(LeveyJenningsPlotOptions form, BindException errors)
{
PropertyManager.PropertyMap current = PropertyManager.getProperties(getUser(), getContainer(), QCFolderConstants.CATEGORY);
PropertyManager.PropertyMap defaults = PropertyManager.getWritableProperties(getContainer(), QCFolderConstants.CATEGORY, true);
PropertyMap current = PropertyManager.getProperties(getUser(), getContainer(), QCFolderConstants.CATEGORY);
WritablePropertyMap defaults = PropertyManager.getWritableProperties(getContainer(), QCFolderConstants.CATEGORY, true);
defaults.clear(); // Clear the map. There may be properties that are no longer applicable (e.g. selectedAnnotations, startDate, endDate).
defaults.putAll(current);
defaults.save();
Expand All @@ -825,7 +828,7 @@ public static class RevertToDefaultQCPlotSettingsAction extends MutatingApiActio
@Override
public Object execute(LeveyJenningsPlotOptions form, BindException errors)
{
PropertyManager.PropertyMap current = PropertyManager.getWritableProperties(getUser(), getContainer(), QCFolderConstants.CATEGORY, false);
WritablePropertyMap current = PropertyManager.getWritableProperties(getUser(), getContainer(), QCFolderConstants.CATEGORY, false);
if (current != null)
{
current.delete();
Expand All @@ -837,7 +840,7 @@ public Object execute(LeveyJenningsPlotOptions form, BindException errors)
}
}

private static class LeveyJenningsPlotOptions
public static class LeveyJenningsPlotOptions
{
private String _metric;
private String _yAxisScale;
Expand Down Expand Up @@ -1306,7 +1309,7 @@ public Object execute(QCMetricOutliersForm form, BindException errors)
response.put("offlineAnnotationTypeId", ts2.getObject(Integer.class));
}

PropertyManager.PropertyMap properties = PropertyManager.getWritableProperties(getUser(), getContainer(), QCFolderConstants.CATEGORY, false);
WritablePropertyMap properties = PropertyManager.getWritableProperties(getUser(), getContainer(), QCFolderConstants.CATEGORY, false);
if (properties != null)
{
Map<String, Object> toSend = new HashMap<>(properties);
Expand Down Expand Up @@ -4158,7 +4161,7 @@ public static class PharmacokineticsOptionsAction extends MutatingApiAction<PKOp
@Override
public Object execute(PKOptions form, BindException errors)
{
PropertyManager.PropertyMap properties = PropertyManager.getWritableProperties(getContainer(), getPropMapName(form), true);
WritablePropertyMap properties = PropertyManager.getWritableProperties(getContainer(), getPropMapName(form), true);

// only stash option properties for users with editor role (i.e. UpdatePermissions)
if (form.getSubgroups() != null && getContainer().hasPermission(getUser(), UpdatePermission.class))
Expand Down
3 changes: 2 additions & 1 deletion src/org/labkey/targetedms/chromlib/ChromatogramLibraryUtils.java
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@
import org.jetbrains.annotations.Nullable;
import org.labkey.api.data.Container;
import org.labkey.api.data.PropertyManager;
import org.labkey.api.data.PropertyManager.WritablePropertyMap;
import org.labkey.api.pipeline.LocalDirectory;
import org.labkey.api.pipeline.PipeRoot;
import org.labkey.api.pipeline.PipelineService;
Expand Down Expand Up @@ -119,7 +120,7 @@ else if (run.getCreated().after(new Date(Files.getLastModifiedTime(clibFile).toM

public static int incrementLibraryRevision(Container container, User user, LocalDirectory localDirectory)
{
PropertyManager.PropertyMap propMap = PropertyManager.getWritableProperties(container, "TargetedMS", true);
WritablePropertyMap propMap = PropertyManager.getWritableProperties(container, "TargetedMS", true);
String revisionVal = propMap.get(PROP_CHROM_LIB_REVISION);
int newRevision;
if(revisionVal == null)
Expand Down
4 changes: 2 additions & 2 deletions src/org/labkey/targetedms/folderImport/PanoramaQCSettings.java
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Original file line number Diff line number Diff line change
@@ -1,7 +1,6 @@
package org.labkey.targetedms.folderImport;

import org.apache.commons.lang3.StringUtils;
import org.apache.jasper.tagplugins.jstl.core.Import;
import org.jetbrains.annotations.NotNull;
import org.jetbrains.annotations.Nullable;
import org.labkey.api.admin.FolderImportContext;
Expand All @@ -12,6 +11,7 @@
import org.labkey.api.data.Container;
import org.labkey.api.data.ContainerFilter;
import org.labkey.api.data.PropertyManager;
import org.labkey.api.data.PropertyManager.WritablePropertyMap;
import org.labkey.api.data.Results;
import org.labkey.api.data.SQLFragment;
import org.labkey.api.data.SimpleFilter;
Expand Down Expand Up @@ -253,7 +253,7 @@ public int importSettingsFromFile(FolderImportContext ctx, VirtualFile panoramaQ
props.load(is);
if (!ctx.getUser().isGuest())
{
PropertyManager.PropertyMap properties = PropertyManager.getWritableProperties(ctx.getUser(), ctx.getContainer(), QCFolderConstants.CATEGORY, true);
WritablePropertyMap properties = PropertyManager.getWritableProperties(ctx.getUser(), ctx.getContainer(), QCFolderConstants.CATEGORY, true);
for (Map.Entry<Object, Object> entry : props.entrySet())
{
if (entry.getKey() instanceof String && entry.getValue() instanceof String)
Expand Down